fasttree: Infer a phylogenetic tree using FastTree

In joelnitta/jntools: Joel Nitta's R Tools

Description

Required FastTree to be installed and on user's PATH.

Usage

fasttree(
  seqs,
  mol_type = "dna",
  model = "gtr",
  gamma = FALSE,
  other_args = NULL,
  echo = FALSE,
  ...
)

Arguments

seqs	DNA alignment of class DNAbin
mol_type	Molecule type; either "dna" or "aa" (proteins)
model	Model to use for phylogenetic analysis. Choose "wag" (WAG+CAT), "lg" (LG+CAT), "gtr" (GTR+CAT), "jc" (Jukes-Cantor + CAT)
gamma	Logical; should branch lengths be rescaled and Gamma20-based likelihood calculated?
other_args	Other arguments to pass to fasttree; must be entered as a character vector with the name and value of each argument separately.
echo	Logical; should STDERR and STDOUT be printed to the screen?
...	Additional arguments; not used by this function.

Value

List of class "phylo".

References

http://www.microbesonline.org/fasttree/

Examples

## Not run: 
library(ape)
data(woodmouse)
fasttree(woodmouse)

## End(Not run)

joelnitta/jntools documentation built on Jan. 17, 2022, 3:05 p.m.